Autoregressive models have transformed protein engineering by enabling the generation of novel protein sequences beyond those found in nature. However, their sequential inference introduces significant latency, limiting their utility in highthroughput protein screening. Speculative decoding accelerates generation by employing a lightweight draft model to sample tokens, which a larger target model then verifies and refines. Yet, in protein sequence generation, draft models are typically agnostic to the structural and functional constraints of the target protein, leading to biologically implausible outputs and a shift in the likelihood distribution of generated sequences. We introduce SpecMER (Speculative Decoding via k-mer Guidance), a novel framework that incorporates biological, structural, and functional priors using k-mer motifs extracted from multiple sequence alignments. By scoring candidate sequences in parallel and selecting those most consistent with known biological patterns, SpecMER significantly improves sequence plausibility while retaining the efficiency of speculative decoding. SpecMER achieves 24-32% speedup over standard autoregressive decoding, along with higher acceptance rates and improved sequence likelihoods.

With the rapid growth of video generative models (VGMs), it is essential to develop reliable and comprehensive automatic metrics for AI-generated videos (AIGVs). Existing methods either use off-the-shelf models optimized for other tasks or rely on human assessment data to train specialized evaluators. These approaches are constrained to specific evaluation aspects and are difficult to scale with the increasing demands for finer-grained and more comprehensive evaluations. To address this issue, this work investigates the feasibility of using multimodal large language models (MLLMs) as a unified evaluator for AIGVs, leveraging their strong visual perception and language understanding capabilities. To evaluate the performance of automatic metrics in unified AIGV evaluation, we introduce a benchmark called UVE-Bench. UVE-Bench collects videos generated by state-of-the-art VGMs and provides pairwise human preference annotations across 15 evaluation aspects. Using UVE-Bench, we extensively evaluate 18 MLLMs. Our empirical results suggest that while advanced MLLMs (e.g., Qwen2VL-72B and InternVL2.5-78B)

Scientific discoveries increasingly rely on complex multimodal reasoning that integrates information-intensive scientific data and domain-specific expertise. Empowered by expert-level scientific benchmarks, scientific Multimodal Large Language Models (MLLMs) hold the potential to significantly enhance this discovery process in realistic workflows. However, current scientific benchmarks mostly focus on evaluating the knowledge understanding capabilities of MLLMs, leading to an inadequate assessment of their perception and reasoning abilities. To address this gap, we present the Scientists First Exam (SFE) benchmark, designed to evaluate the scientific cognitive capacities of MLLMs through three cognitive levels: scientific signal perception, scientific attribute understanding, scientific comparative reasoning. Specifically, SFE comprises 830 expert-verified VQA pairs across three question types, spanning 66 multimodal tasks across five high-value disciplines. Extensive experiments reveal that current state-of-the-art GPT-o3 and InternVL-3 achieve only 34.08% and 26.52% on SFE, highlighting significant room for MLLMs to improve in scientific realms. We hope the insights obtained in SFE will facilitate further developments in AI-enhanced scientific discoveries.

Inspired by the remarkable success of foundation models in language and vision, Graph Foundation Models (GFMs) hold significant promise for broad applicability across diverse graph tasks and domains. However, existing GFMs struggle with unstable few-shot fine-tuning, where both performance and adaptation efficiency exhibit significant fluctuations caused by the randomness in the support sample selection and structural discrepancies between the pre-trained and target graphs. How to fine-tune GFMs robustly and efficiently to enable trustworthy knowledge transfer across domains and tasks is the major challenge. In this paper, we propose GRAVER, a novel Generative gRAph VocabulariEs for Robust GFM fine-tuning framework that tackles the aforementioned instability via generative augmentations. Specifically, to identify transferable units, we analyze and extract key class-specific subgraph patterns by ego-graph disentanglement and validate their transferability both theoretically and empirically. To enable effective pre-training across diverse domains, we leverage a universal task template based on ego-graph similarity and construct graph vocabularies via graphon-based generative experts. To facilitate robust and efficient prompt fine-tuning, we grave the support samples with in-context vocabularies, where the lightweight MoE-CoE network attentively routes knowledge from source domains. Extensive experiments demonstrate the superiority of GRAVER over effectiveness, robustness, and efficiency on downstream few-shot node and graph classification tasks compared with 15 state-of-the-art baselines.

Open-Vocabulary Segmentation (OVS) aims to segment classes that are not present in the training dataset. However, most existing studies assume that the training data is fixed in advance, overlooking more practical scenarios where new datasets are continuously collected over time. To address this, we first analyze how existing OVS models perform under such conditions. In this context, we explore several approaches such as retraining, fine-tuning, and continual learning but find that each of them has clear limitations. To address these issues, we propose ConOVS, a novel continual learning method based on a Mixture-of-Experts framework. ConOVS dynamically combines expert decoders based on the probability that an input sample belongs to the distribution of each incremental dataset. Through extensive experiments, we show that ConOVS consistently outperforms existing methods across pre-training, incremental, and zero-shot test datasets, effectively expanding the recognition capabilities of OVS models when data is collected sequentially.

We investigate fingerprints in pretraining datasets for large language models (LLMs) through dataset classification experiments. Building on prior work demonstrating the existence of fingerprints or biases in popular computer vision datasets, we analyze popular open-source pretraining datasets for LLMs derived from CommonCrawl including C4, RefinedWeb, DolmaCC, RedPajama-V2, FineWeb, and DCLM-Baseline. Despite those datasets being obtained with similar curation steps, neural networks can classify surprisingly well which dataset a single text sequence belongs to, significantly better than a human can. This indicates that small differences in filtering and processing pipelines induce fingerprints, that we find are evident in formatting, vocabulary, and content distributions. Such fingerprints can negatively impact cross-dataset generalization. Additionally, we show that these fingerprints propagate through training: sequences generated by models trained on those datasets can be accurately classified by a classifier trained on the original datasets. This can offer insights into data characteristics that are typically undisclosed by LLM developers, including pretraining mixture proportions and finetuning data sources.

Existing prompting and supervised fine-tuning (SFT) methods remain fixed by prompt rules or training corpora, and are usually benchmarked only on wellstructured wiki sources, limiting real-world adaptability. We introduce WebPuzzle, a 24k-sample training and 275-sample test benchmark that evaluates information seeking on the live internet, across both wiki and open-domain queries. Leveraging 7k WebPuzzle instances, we develop DeepDiver, a reinforcement-learning (RL) framework that cultivates Search Intensity Scaling (SIS)--an emergent ability to escalate search frequency and depth instead of settling on overconfident, underevidenced answers. With SIS, Qwen2.5-7B-Instruct and Pangu-7B-Reasoner attain performance on real-web tasks comparable to the 671B-parameter DeepSeek-R1. We detail DeepDiver's curriculum from cold-start SFT to a well designed RL procedure, and show that its seeking policy generalized from closed-ended queries to open-ended generation such as long-form writing. Our results advance adaptive information seeking in LLMs and provide a rigorous benchmark for future work.

We address the problem of incremental sequence classification, where predictions are updated as new elements in the sequence are revealed. Drawing on temporaldifference learning from reinforcement learning, we identify a temporal-consistency condition that successive predictions should satisfy. We leverage this condition to develop a novel loss function for training incremental sequence classifiers. Through a concrete example, we demonstrate that optimizing this loss can offer substantial gains in data efficiency. We apply our method to text classification tasks and show that it improves predictive accuracy over competing approaches on several benchmark datasets. We further evaluate our approach on the task of verifying large language model generations for correctness in grade-school math problems. Our results show that models trained with our method are better able to distinguish promising generations from unpromising ones after observing only a few tokens.

While humans effortlessly draw visual objects and shapes by adaptively allocating attention based on their complexity, existing multimodal large language models (MLLMs) remain constrained by rigid token representations. Bridging this gap, we propose ALTo, an adaptive-length tokenizer for autoregressive mask generation. To achieve this, a novel token length predictor is designed, along with a length regularization term and a differentiable token chunking strategy.

Transformers are increasingly prevalent for multiview computer vision tasks, where geometric relationships between viewpoints are critical for 3D perception. To leverage these relationships, multiview transformers must use camera geometry to ground visual tokens in 3D space. In this work, we compare techniques for conditioning transformers on cameras: token-level raymap encodings, attentionlevel relative pose encodings, and a new relative encoding--Projective Positional Encoding (PRoPE)--that captures complete camera frustums, both intrinsics and extrinsics, as a relative positional encoding. Our experiments begin by showing how relative conditioning methods improve performance in feedforward novel view synthesis, with further gains from PRoPE. This holds across settings: scenes with both shared and varying intrinsics, when combining token-and attention-level conditioning, and for generalization to inputs with out-of-distribution sequence lengths and camera intrinsics. We then verify that these benefits persist for different tasks, stereo depth estimation and discriminative spatial cognition, as well as larger model sizes. Code is available on our project webpage2.